From 285e7c8ecf564540300d1fab1287ba4581cd6cf8 Mon Sep 17 00:00:00 2001 From: Neil Horner Date: Wed, 26 Jul 2023 21:09:29 +0000 Subject: [PATCH] Remove unused parameter --- .gitlab-ci.yml | 6 +++--- README.md | 9 +++++---- docs/quickstart.md | 9 +++++---- 3 files changed, 13 insertions(+), 11 deletions(-) diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index dd1b9d1..9b63f50 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -89,7 +89,7 @@ docker-run: --ref_annotation differential_expression/gencode.v22.annotation.chr20.gff \ --direct_rna --minimap_index_opts '-k 15' \ --ref_transcriptome differential_expression/ref_transcriptome.fasta \ - --transcriptome_assembly false --sample_sheet test_data/sample_sheet.csv" + --sample_sheet test_data/sample_sheet.csv" NF_IGNORE_PROCESSES: > preprocess_reads,merge_transcriptomes,assemble_transcripts,decompress_annotation,decompress_ref, build_minimap_index,get_transcriptome,merge_gff_bundles,run_gffcompare,build_minimap_index,split_bam @@ -103,7 +103,7 @@ docker-run: --ref_annotation differential_expression/gencode.v22.annotation.chr20.gff3 \ --direct_rna --minimap_index_opts '-k 15' \ --ref_transcriptome differential_expression/ref_transcriptome.fasta \ - --transcriptome_assembly false --sample_sheet test_data/sample_sheet.csv" + --sample_sheet test_data/sample_sheet.csv" NF_IGNORE_PROCESSES: > preprocess_reads,merge_transcriptomes,assemble_transcripts,decompress_annotation,decompress_ref, build_minimap_index,get_transcriptome,merge_gff_bundles,run_gffcompare,build_minimap_index,split_bam @@ -117,7 +117,7 @@ docker-run: --ref_genome differential_expression_ncbi/GRCh38.p14.NCBI_test.fna.gz \ --ref_annotation differential_expression_ncbi/GRCh38.p14_NCBI_test.gtf.gz \ --direct_rna --minimap_index_opts '-w 25' \ - --transcriptome_assembly false --sample_sheet test_data/sample_sheet.csv" + --sample_sheet test_data/sample_sheet.csv" NF_IGNORE_PROCESSES: > preprocess_reads,merge_transcriptomes,assemble_transcripts, build_minimap_index,get_transcriptome,merge_gff_bundles,run_gffcompare,build_minimap_index,split_bam diff --git a/README.md b/README.md index 1925c14..7190350 100644 --- a/README.md +++ b/README.md @@ -241,7 +241,8 @@ nextflow run epi2me-labs/wf-transcriptomes \ --de_analysis \ --ref_genome differential_expression/hg38_chr20.fa \ --ref_annotation differential_expression/gencode.v22.annotation.chr20.gtf \ - --direct_rna --minimap_index_opts \-k15 + --direct_rna --minimap_index_opts \ + -k15 ``` You can also run the differential expression section of the workflow on its own by providing a reference transcriptome and setting the transcriptome assembly parameter to false. eg. @@ -251,9 +252,9 @@ nextflow run epi2me-labs/wf-transcriptomes \ --de_analysis \ --ref_genome differential_expression/hg38_chr20.fa \ --ref_annotation differential_expression/gencode.v22.annotation.chr20.gtf \ - --direct_rna --minimap_index_opts \-k15 \ - --ref_transcriptome differential_expression/ref_transcriptome.fasta \ - --transcriptome_assembly false + --direct_rna --minimap_index_opts \ + -k15 \ + --ref_transcriptome differential_expression/ref_transcriptome.fasta ``` ## Workflow outputs diff --git a/docs/quickstart.md b/docs/quickstart.md index 9d92026..0726236 100644 --- a/docs/quickstart.md +++ b/docs/quickstart.md @@ -151,7 +151,8 @@ nextflow run epi2me-labs/wf-transcriptomes \ --de_analysis \ --ref_genome differential_expression/hg38_chr20.fa \ --ref_annotation differential_expression/gencode.v22.annotation.chr20.gtf \ - --direct_rna --minimap_index_opts \-k15 + --direct_rna --minimap_index_opts \ + -k15 ``` You can also run the differential expression section of the workflow on its own by providing a reference transcriptome and setting the transcriptome assembly parameter to false. eg. @@ -161,9 +162,9 @@ nextflow run epi2me-labs/wf-transcriptomes \ --de_analysis \ --ref_genome differential_expression/hg38_chr20.fa \ --ref_annotation differential_expression/gencode.v22.annotation.chr20.gtf \ - --direct_rna --minimap_index_opts \-k15 \ - --ref_transcriptome differential_expression/ref_transcriptome.fasta \ - --transcriptome_assembly false + --direct_rna --minimap_index_opts \ + -k15 \ + --ref_transcriptome differential_expression/ref_transcriptome.fasta ``` ## Workflow outputs